Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow, Russian Federation.
ITMO University, Saint Petersburg, Russian Federation.
Bioinformatics. 2018 Feb 1;34(3):434-444. doi: 10.1093/bioinformatics/btx681.
Antibiotic resistance is an important global public health problem. Human gut microbiota is an accumulator of resistance genes potentially providing them to pathogens. It is important to develop tools for identifying the mechanisms of how resistance is transmitted between gut microbial species and pathogens.
We developed MetaCherchant-an algorithm for extracting the genomic environment of antibiotic resistance genes from metagenomic data in the form of a graph. The algorithm was validated on a number of simulated and published datasets, as well as applied to new 'shotgun' metagenomes of gut microbiota from patients with Helicobacter pylori who underwent antibiotic therapy. Genomic context was reconstructed for several major resistance genes. Taxonomic annotation of the context suggests that within a single metagenome, the resistance genes can be contained in genomes of multiple species. MetaCherchant allows reconstruction of mobile elements with resistance genes within the genomes of bacteria using metagenomic data. Application of MetaCherchant in differential mode produced specific graph structures suggesting the evidence of possible resistance gene transmission within a mobile element that occurred as a result of the antibiotic therapy. MetaCherchant is a promising tool giving researchers an opportunity to get an insight into dynamics of resistance transmission in vivo basing on metagenomic data.
Source code and binaries are freely available for download at https://github.com/ctlab/metacherchant. The code is written in Java and is platform-independent.
Supplementary data are available at Bioinformatics online.
抗生素耐药性是一个重要的全球公共卫生问题。人类肠道微生物群是耐药基因的聚集地，这些基因可能会将其提供给病原体。因此，开发工具以确定抗生素耐药性在肠道微生物物种和病原体之间传播的机制非常重要。
我们开发了 MetaCherchant，这是一种从宏基因组数据中以图形形式提取抗生素耐药基因基因组环境的算法。该算法在多个模拟和已发表的数据集上进行了验证，同时也应用于接受抗生素治疗的幽门螺杆菌患者肠道微生物群的新“shotgun”宏基因组。重建了几个主要耐药基因的基因组环境。对上下文的分类注释表明，在单个宏基因组中，耐药基因可以包含在多个物种的基因组中。MetaCherchant 允许使用宏基因组数据重建带有耐药基因的移动元件内的细菌基因组。MetaCherchant 在差分模式下的应用产生了特定的图形结构，表明抗生素治疗导致移动元件内可能发生耐药基因传播的证据。MetaCherchant 是一种很有前途的工具，它使研究人员有机会根据宏基因组数据深入了解体内耐药性传播的动态。
源代码和二进制文件可在 https://github.com/ctlab/metacherchant 上免费下载。该代码是用 Java 编写的，与平台无关。
补充数据可在“Bioinformatics”在线获取。
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